ArticleJournal of chemical information and modeling2025
Free Energy Perturbation Simulations Measure the Change in Binding Affinity of the Aβ25-35 Peptide to the Zwitterionic Bilayer Caused by Oxidation.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
We designed and employed a relative free energy perturbation (FEP) combined with replica exchange with solute tempering (REST) all-atom molecular dynamics to investigate how Met35 oxidation affects the free energy of binding of the Aβ25-35 peptide to the DMPC lipid bilayer. We first showed that our restraint-free FEP/REST protocol delivers a converged sampling of alchemical transformations in the DMPC bilayer and in lipid-free water. Then, we determined that Met35 oxidation moderately reduced the peptide binding free energy by ΔΔ
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